Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate 3608924 Dshi_2314 Pyridoxal-5'-phosphate-dependent protein beta subunit (RefSeq)
Query= BRENDA::A0A0F6AQU1 (342 letters) >FitnessBrowser__Dino:3608924 Length = 345 Score = 488 bits (1257), Expect = e-143 Identities = 233/330 (70%), Positives = 277/330 (83%), Gaps = 2/330 (0%) Query: 2 FNSVLDTIGNTPLIRLSKASELTGCDIYGKAEFLNPGQSVKDRAALYIIRDAEKRGLLRP 61 + + + IG+TPLIRL+ ASE TGC+I GKAEFLNPGQSVKDRAALYIIRDA RG L+P Sbjct: 4 YRDLAEAIGHTPLIRLNAASEATGCEILGKAEFLNPGQSVKDRAALYIIRDAVARGTLKP 63 Query: 62 GGVIVEGTAGNTGIGLTMVAKALGYRTAIVIPETQSQEKKDALRLLGAELIEVPAAPYRN 121 GG IVEGTAGNTGIGL +V ++G++T IVIPETQS+EKKD LRL GA+L++VPAAPYRN Sbjct: 64 GGTIVEGTAGNTGIGLALVGASMGFKTVIVIPETQSEEKKDMLRLAGADLVQVPAAPYRN 123 Query: 122 PNNYVRLSGRLAEQLAKTEPNGAIWANQFDNTVNRQAHIETTAQEIWRDTSDQIDGFVAA 181 PNNYVR S RLA++LA+TEP+GAIWANQFDN NRQAH+ETT EIW T ++DGF+ A Sbjct: 124 PNNYVRYSERLAKRLAETEPHGAIWANQFDNVANRQAHVETTGPEIWDQTGGKVDGFICA 183 Query: 182 VGSGGTLAGTAIGLKERNHNIKIALADPHGAALHAFYTTGELKAEGDSITEGIGQGRITA 241 GSGGT+AG + L+ + +K+ LADP GAAL+ FYT GELK+EG SI+EGIGQGRITA Sbjct: 184 AGSGGTVAGVGLALQPK--GVKVGLADPDGAALYNFYTQGELKSEGSSISEGIGQGRITA 241 Query: 242 NLEGFTPDFSYQIPDAEALDILFALVEEEGLCLGGSSGINIAGAIRLAKDLGPGHTIVTV 301 NLEGFTPDF+ +PD+EAL I+F L+ EG+CLGGSSGINIAGAIR+A+ +GPGHTIVT+ Sbjct: 242 NLEGFTPDFACNVPDSEALPIVFDLLRHEGICLGGSSGINIAGAIRMARHMGPGHTIVTI 301 Query: 302 LCDYGNRYQSKLFNPAFLRGKSLPVPRWLE 331 LCDYG RYQSKLFNP FLR K LPVP WL+ Sbjct: 302 LCDYGTRYQSKLFNPDFLRSKDLPVPDWLD 331 Lambda K H 0.316 0.137 0.398 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 463 Number of extensions: 15 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 342 Length of database: 345 Length adjustment: 29 Effective length of query: 313 Effective length of database: 316 Effective search space: 98908 Effective search space used: 98908 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory